Ontology highlight
ABSTRACT:
PROVIDER: PRJNA838276 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:The yeast strain Moniliella spathulata SBUG-Y 2180 was isolated from oil-contaminated soil at the Tengiz oil field in the Atyrau region of Kazakhstan on the basis of its unique ability to use crude oil and its components as the sole carbon and energy source. This yeast used a large number of hydrocarbons as substrates (more than 150), including n-alkanes with chain lengths ranging from C10 to C32, monomethyl- and monoethyl-substituted alkanes (C9 – C23), n-alkylcyclo alkanes with alkyl chain lengths from 3 to 24 carbon atoms as well as substituted monoaromatic and diaromatic hydrocarbons. Metabolism of this huge range of hydrocarbon substrates produced a very large number of aliphatic, alicyclic and aromatic acids. 51 of these were identified by GC/MS analyses. This is the first report of the degradation and of the formation of such a large number of compounds by a yeast. Inoculation of barley seeds with M. spathulata SBUG-Y 2180 had a positive effect on shoot and root development of plants grown in oil-contaminated sand, pointing towards potential applications of the yeast in bioremediation of polluted soils.
2021-02-15 | PXD022543 | Pride
Project description:The mycobacterial cell wall is a distinctive thick layer that protects the tubercle bacillus from general antibiotics and the host’s immune system. Mycolic acids, which are long-chain α-alkyl-β-hydroxy fatty acids, are the major constituents of this protective layer, and their synthesis has been shown to be critical for the survival of M. tuberculosis. This model captures the mycolic acid pathway in M. tuberculosis with 197 metabolites participating in 219 reactions catalysed by 28 proteins. The model helps in the rational identification of potential anti-tubercular drug targets.
2024-09-02 | BIOMD0000001046 | BioModels
Project description:The Baltic Sea is one of the largest brackish water bodies in the world. Redoxclines that form between oxic and anoxic layers in the deepest sub-basins are a semi-permanent character of the pelagic Baltic Sea. The microbially mediated nitrogen removal processes in these redoxclines have been recognized as important ecosystem service that removes large proportion of the nitrogen load originating from the drainage basin. However, nitrification, which links mineralization of organic nitrogen and nitrogen removal processes, has remained poorly understood. To gain better understanding of the nitrogen cycling in the Baltic Sea, we analyzed the assemblage of ammonia oxidizing bacteria and archaea in the central Baltic Sea using functional gene microarrays and measured the biogeochemical properties along with potential nitrification rates. Overall, the ammonia oxidizer communities in the Baltic Sea redoxcline were very evenly distributed. However, the communities were clearly different between the eastern and western Gotland Basin and the correlations between different components of the ammonia oxidizer assemblages and environmental variables suggest ecological basis for the community composition. The more even community ammonia oxidizer composition in the eastern Gotland Basin may be related to the constantly oscillating redoxcline that does not allow domination of single archetype. The oscillating redoxcline also creates long depth range of optimal nitrification conditions. The rate measurements suggest that nitrification in the central Baltic Sea is able to produce all nitrate required by denitrification occurring below the nitrification zone.
2013-08-24 | GSE50164 | GEO
Project description:The ecophysiology of complete ammonia oxidizing Nitrospira (CMX) and their widespread occurrence in groundwater suggests that CMX bacteria have a competitive advantage over ammonia-oxidizing bacteria (AOB) and archaea (AOA) in these environments. However, the relevance of their activity from the ecosystem-level process perspective has remained unclear. We investigated oligotrophic carbonate rock aquifers as a model system to assess the contribution of CMX, AOA and AOB to nitrification and to identify the environmental drivers of their niche differentiation at different levels of ammonium and oxygen. CMX accounted for up to 95% of the ammonia oxidizer communities. Nitrification rates were positively correlated to CMX clade A-associated phylotypes and AOB affiliated with Nitrosomonas ureae. Surprisingly, short-term incubations amended with the nitrification inhibitors allylthiourea and chlorate suggested that AOB contributed more than 90% to overall ammonia oxidation, while metaproteomics analysis confirmed an active role of CMX in both ammonia and nitrite oxidation. Ecophysiological niche differentiation of CMX clades A and B, AOA and AOB was linked to their requirements for ammonium, oxygen tolerance, and metabolic versatility. Our results demonstrate that despite numerical predominance of CMX, the first step of nitrification in oligotrophic groundwater is primarily governed by AOB. Higher growth yields at lower NH4+ turnover rates and energy derived from nitrite oxidation most likely enable CMX to maintain consistently high populations. Activity measurements combined with differential inhibition allowed a refined understanding of ammonia oxidizer coexistence, competition and cooperation beyond the insights from molecular data alone.
2023-10-24 | PXD039573 | Pride
Project description:Studies of herpes simplex virus (HSV) entry revealed a previously unrecognized "outside-in" signaling pathway involving phosphatidylserine (PS) scrambling and associated translocation and subsequent extracellular activation of canonical intracellular proteins, including Akt. We hypothesized that HIV-1, which activates a different scramblase, TMEM16F, to induce PS externalization, may similarly trigger an "outside-in" signaling response to promote viral entry. To study this process, we utilized a cell-impermeable staurosporine analog, alkyl-CIMSS, which is a broadly active kinase inhibitor that blocks HSV-induced exofacial Akt phosphorylation, and HSV entry. We show that TMEM16F-mediated PS externalization in response to HIV is not associated with Akt translocation; however, surprisingly, pretreatment of cells with alkyl-CIMSS enhanced HIV-1 infection post-entry. To identify potential biological processes that mediated this enhancement, we performed whole-cell total and phosphoproteomics, and bulk RNA sequencing. Cells treated with alkyl-CIMSS exhibited increased cyclin-dependent kinase (CDK) activity, resulting in higher levels of phosphorylated SAMHD1. Further, alkyl-CIMSS treatment robustly upregulated the cell surface density of the proteoglycan glypican-1 (GPC1). Lentivirus-driven GPC1 overexpression or shRNA knockdown demonstrated that, independent of alkyl-CIMSS treatment, GPC1 expression promotes HIV infection. Collectively, these findings demonstrate that alkyl-CIMSS modulates the exofacial plasma membrane to promote susceptibility to HIV infection by increasing CDK activity and upregulating GPC1.
2026-04-01 | GSE325970 | GEO